Descripción del proyecto
Regulación genética y función del genoma tridimensional
La organización tridimensional del genoma dentro del núcleo celular, denominada genoma 3D, es fundamental para la regulación genética. Se han identificado los componentes principales del genoma 3D, pero aún se desconoce su contribución a la regulación genética. El objetivo del proyecto financiado con fondos europeos FuncDis3D es investigar funcionalmente el genoma 3D en aras de comprender su papel en la expresión génica. El método consiste en inducir cambios en el genoma 3D mediante la eliminación de proteínas y evaluar estos cambios a lo largo del tiempo. Los datos preliminares revelan que la eliminación de reguladores del genoma 3D conlleva que los cambios ocurran en unas pocas horas. Los investigadores eliminarán un rango de proteínas en células pluripotentes y diferenciadas para determinar su participación en la organización del genoma 3D. La caracterización simultánea del epigenoma y del transcriptoma les permitirá determinar la secuencia de cambios.
Objetivo
The three-dimensional organization of the genome inside the nucleus (3DG) is crucial for gene regulation. Although the fundamental building blocks of the 3DG have been identified, how they contribute to gene regulation is incompletely understood. In recent years my lab has started to functionally dissect the 3DG in order to understand the effects on gene expression. The current proposal intends to expand this work and aims to i) broaden the array of proteins that are known organize the 3DG, ii) determine how loss of these proteins affects the 3DG and iii) elucidate how this influences gene expression.
The key to this is to induce changes in the 3DG by acute protein depletion and measuring changes over time. We have preliminary data showing that by depleting regulators of the 3DG we can induce changes within a few hours. We will deplete a range of proteins in pluripotent and differentiated cells to determine their contribution to 3DG organization. Simultaneous characterization of the epigenome and transcriptome will allow us to determine the sequence of changes. In addition, we will perform Thousands of Reporters Integrated in Parallel (TRIP) after perturbation of the 3DG. TRIP reporters all have the same minimal promoter that acts as a sensor for promoter-enhancer (mis)-communication. By combining TRIP with 4C we can measure the changes in the reporter-enhancer interaction landscape. Our data will generate fundamental insight into the parameters that govern the interactions between promoters and regulatory elements, within the context of the 3DG, and their effects on gene expression. Furthermore, it allows us to determine the temporal order of changes in the 3DG, the epigenome and gene expression, which is essential for the establishment of cause-and-effect relationships. Collectively, our data will lead to a better appreciation of how distal and proximal regulatory regions cooperate to establish cell-type specific gene expression programs.
Ámbito científico
Programa(s)
Régimen de financiación
ERC-COG - Consolidator GrantInstitución de acogida
1066 CX Amsterdam
Países Bajos